Python-Dronekit script on iMX6 and Mission Planner

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I'm in the extremely early stages of building an app that uses the USB payload connector to receive data from a payload radio receiver (not in any way controlling the aircraft) and log it, along with flight telemetry to a .csv file. If I use the iMX6 to receive the data and log it can I still use Mission Planner to build the flight plan and upload to the Pixhawk? In addition I may want to adjust receiver frequency at each sample point, which might require some time to change frequency on the receiver. Once a waypoint mission begins can the iMX6 pause/interrupt the mission to perform a task then let it continue?

Basic format would be something along the lines of LAT,LON,ALT,FREQ(optional),RECV-SNR,RECV-PWR. Sample period would be every 100-300 ft or so depending on test results.
 
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If you change the mode to auto or loiter, do your stuff, and then change to guided once it's done, I believe it should just continue the mission.
I think you also need to make sure that throttle is not to low
 
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